Unraveling UVB effects: Catalase activity and molecular alterations in the stratum corneum.

AIM: Ultraviolet B (UVB) radiation can compromise the functionality of the skin barrier through various mechanisms. We hypothesize that UVB induce photochemical alterations in the components of the outermost layer of the skin, known as the stratum corneum (SC), and modulate its antioxidative defense mechanisms. Catalase is a well-known antioxidative enzyme found in the SC where it acts to scavenge reactive oxygen species. However, a detailed characterization of acute UVB exposure on the activity of native catalase in the SC is lacking. Moreover, the effects of UVB irradiation on the molecular dynamics and organization of the SC keratin and lipid components remain unclear. Thus, the aim of this work is to characterize consequences of UVB exposure on the structural and antioxidative properties of catalase, as well as on the molecular and global properties of the SC matrix surrounding the enzyme. EXPERIMENTS: The effect of UVB irradiation on the catalase function is investigated by chronoamperometry with a skin covered oxygen electrode, which probes the activity of native catalase in the SC matrix. Circular dichroism is used to explore changes of the catalase secondary structure, and gel electrophoresis is used to detect fragmentation of the enzyme following the UVB exposure. UVB induced alterations of the SC molecular dynamics and structural features of the SC barrier, as well as its water sorption behavior, are investigated by a complementary set of techniques, including natural abundance 13C polarization transfer solid-state NMR, wide-angle X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, and dynamic vapor sorption microbalance. FINDINGS: The findings show that UVB exposure impairs the antioxidative function of catalase by deactivating both native catalase in the SC matrix and lyophilized catalase. However, UVB radiation does not alter the secondary structure of the catalase nor induce any observable enzyme fragmentation, which otherwise could explain deactivation of its function. NMR measurements on SC samples show a subtle increase in the molecular mobility of the terminal segments of the SC lipids, accompanied by a decrease in the mobility of lipid chain trans-gauche conformers after high doses of UVB exposure. At the same time, the NMR data suggest increased rigidity of the polypeptide backbone of the keratin filaments, while the molecular mobility of amino acid residues in random coil domains of keratin remain unaffected by UVB irradiation. The FTIR data show a consistent decrease in absorbance associated with lipid bond vibrations, relative to the main protein bands. Collectively, the NMR and FTIR data suggest a small modification in the composition of fluid and solid phases of the SC lipid and protein components after UVB exposure, unrelated to the hydration capacity of the SC tissue. To conclude, UVB deactivation of catalase is anticipated to elevate oxidative stress of the SC, which, when coupled with subtle changes in the molecular characteristics of the SC, may compromise the overall skin health and elevate the likelihood of developing skin disorders.

Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase.

Catalase is an antioxidant enzyme that breaks down hydrogen peroxide (H2O2) into molecular oxygen and water. In all monofunctional catalases the pathway that H2O2 takes to the catalytic centre is via the `main channel'. However, the structure of this channel differs in large-subunit and small-subunit catalases. In large-subunit catalases the channel is 15 Šlonger and consists of two distinct parts, including a hydrophobic lower region near the heme and a hydrophilic upper region where multiple H2O2 routes are possible. Conserved glutamic acid and threonine residues are located near the intersection of these two regions. Mutations of these two residues in the Scytalidium thermophilum catalase had no significant effect on catalase activity. However, the secondary phenol oxidase activity was markedly altered, with kcat and kcat/Km values that were significantly increased in the five variants E484A, E484I, T188D, T188I and T188F. These variants also showed a lower affinity for inhibitors of oxidase activity than the wild-type enzyme and a higher affinity for phenolic substrates. Oxidation of heme b to heme d did not occur in most of the studied variants. Structural changes in solvent-chain integrity and channel architecture were also observed. In summary, modification of the main-channel gate glutamic acid and threonine residues has a greater influence on the secondary activity of the catalase enzyme, and the oxidation of heme b to heme d is predominantly inhibited by their conversion to aliphatic and aromatic residues.

SDBS induces multiple catalase conformations in a dose-dependent manner.

Amyloid fibrils have been linked to several incurable diseases. They are long and thin fibrous proteins that self-assemble into fibrils. Small molecules can stimulate amyloid fibrillation, but the mechanism by which this happens is not well understood. This study examined how a negatively charged benzene ring containing surfactant, sodium dodecylbenzene sulphonate (SDBS), affects the fibrillation of bovine liver catalase (BLC). After SDBS treatment, BLC conformational changes were examined in vitro using turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM. BLC in the native state was alpha-helical at pH 7.4, while it was converted to a random coil structure at pH 2.0. Far-UV CD and intrinsic fluorescence data showed that at concentrations <0.1 mM of SDBS, randomly coiled BLC assumed a native-like alpha-helical structure. However, between 0.1 and 1.0 mM SDBS, BLC was aggregated. ThT fluorescence and far-UV CD measurements showed the amyloid-like structures in the aggregated BLC. At higher SDBS concentrations (>1.0 mM) at pH 2.0, BLC again attains a native-like alpha-helical structure. It is essential for therapeutic purposes to clearly understand the process underlying surfactant- or lipid-induced fibrillation.

Rv1255c, a dormancy-related transcriptional regulator of TetR family in Mycobacterium tuberculosis, enhances isoniazid tolerance in Mycobacterium smegmatis.

Mycobacterium tuberculosis is exposed to diverse stresses inside the host during dormancy. Meanwhile, many metabolic and transcriptional regulatory changes occur, resulting in physiological modifications that help M. tuberculosis to adapt to these stresses. The same physiological changes also cause antibiotic tolerance in dormant M. tuberculosis. However, the transcriptional regulatory mechanism of antibiotic tolerance during dormancy remains unclear. Here, we showed that the expression of Rv1255c, an uncharacterised member of the tetracycline repressor family of transcriptional regulators, is upregulated during different stresses and hypoxia-induced dormancy. Antibiotic tolerance and efflux activities of Mycobacterium smegmatis constitutively expressing Rv1255c were analysed, and interestingly, it showed increased isoniazid tolerance and efflux activity. The intrabacterial isoniazid concentrations were found to be low in M. smegmatis expressing Rv1255c. Moreover, orthologs of the M. tuberculosis katG, gene of the enzyme which activates the first-line prodrug isoniazid, are overexpressed in this strain. Structural analysis of isoforms of KatG enzymes in M. smegmatis identified major amino acid substitutions associated with isoniazid resistance. Thus, we showed that Rv1255c helps M. smegmatis tolerate isoniazid by orchestrating drug efflux machinery. In addition, we showed that Rv1255c also causes overexpression of katG isoform in M. smegmatis which has amino acid substitutions as found in isoniazid-resistant katG in M. tuberculosis.

Bovine liver catalase turns into three conformational states after exposure to an anionic surfactant.

The mechanism by which anionic surfactants promote amyloid fibril is not well understood. Here, we investigated how sodium dodecyl sulfate (SDS), a negatively charged surfactant, affects the fibrillation of the partially unfolded random-coiled bovine liver catalase (BLC) at a pH of 2.0. We used several methods, including turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM imaging, to evaluate the conformational changes of BLC in vitro in response to SDS treatment. BLC is a multimeric protein and well folded at physiological pH but forms a random coil structure at pH 2.0. Intrinsic fluorescence and far-UV CD data showed that below 0.1 mM SDS, random coiled BLC turned into a native-like structure. BLC incubated with an SDS concentration ranging from 0.1 to 2.0 mM led to the formation of aggregates. The ThT fluorescence intensity was enhanced in the aggregated BLC samples (0.1-2.0 mM SDS), and cross beta-sheeted structure was detected by the far UV CD measurements. BLC adopts a complete alpha-helical structure upon interacting with SDS at a more than 2.0 mM concentration at pH 2.0. Understanding the mechanism of surfactant- or lipid-induced fibrillation is important for therapeutic purposes.

Nanozyme can substitute a natural Ogataea polymorpha catalase enzyme in vivo.

Nanomaterials possessing artificial, enzyme-like catalytic activity (nanozymes, NZs) have a great potential for application in research, immunological assays, biosensors, in vivo imaging, and as therapeutic agents. Despite the obvious advances in construction and understanding of functional properties of NZs, there is still no clear evidence of whether they can complement the loss of corresponding enzymatic activity in vivo. Herein, we report the first, to the best to our knowledge, example of successful substitution of natural enzyme activity by catalase-like platinum (nPt) and platinum-gold (nPtAu) nanoparticles transferred to the cells of methylotrophic yeast Ogataea polymorpha. The nPt NZs were synthesized by the chemical reduction method and used as a seed to produce the nPt(core)Au(shell) particles. The produced nPt NZs were 68.1 and 91.3 nm in size, while the hydrids were of 531.2 and 615.1 nm. Both nPt and nPtAu demonstrated catalase activity in vitro. The catalase-deficient strain Ogataea polymorpha C-105 was shown to be able to grow on methanol and a mixture of glucose and methanol in the presence although not in the absence of NZs, this correlating with the decrease in intracellular hydrogen peroxide production. The results provide the first example of complementation of the natural enzyme function by synthetic NZs, the phenomenon which can further be used in a screening for new catalase-like nanozymes and as a fruitful tool to modify living cells by nanoparticles possessing catalytic activity and to use such modified cells as sensitive elements in cell-based biosensors.

Missing-Linker-Confined Single-Atomic Pt Nanozymes for Enzymatic Theranostics of Tumor.

Conventional nanozymes often possess low active site density. Pursuing effective strategies for constructing highly active single-atomic nanosystems with maximum atom utilization efficiency is exceptionally attractive. Herein, we develop a facile "missing-linker-confined coordination" strategy to fabricate two self-assembled nanozymes, i.e., conventional nanozyme (NE) and single-atomic nanozyme (SAE), which respectively consist of Pt nanoparticles and single Pt atoms as active catalytic sites anchored in metal-organic frameworks (MOFs) with encapsulated photosensitizers for catalase-mimicking enhanced photodynamic therapy. Compared to a Pt nanoparticle-based conventional nanozyme, a Pt single-atomic nanozyme shows enhanced catalase-mimicking activity in generating oxygen for overcoming tumor hypoxia, thus exhibiting a more efficient reactive oxygen species generation and high tumor inhibition rate.

Multienzyme-Mimicking Au@Cu2O with Complete Antioxidant Capacity for Reactive Oxygen Species Scavenging.

Most enzyme catalysts are unable to achieve effective oxidation resistance because of the monotonous mimicking function or production of secondary reactive oxygen species (ROS). Herein, the Au@Cu2O heterostructure with multienzyme-like activities is deigned, which has significantly improved antioxidant capacity compared with pure Cu2O for the scavenging of highly cell-damaging secondary ROS, i.e.,·OH. Experiments and theoretical calculations show that the heterostructure exhibits a built-in electric field and lattice mismatch at the metal-semiconductor interface, which facilitate to generate abundant oxygen vacancies, redox couples, and surface electron deficiency. On the one hand, the presence of rich oxygen vacancies and redox couple can enhance the adsorption and activation of oxygen-containing ROS (including O2·- and H2O2). On the other hand, the electron transfer between the electron-deficient Au@Cu2O surface and electron donor would promote peroxide-like activity and avoid producing ·OH. Importantly, endogenous ·OH could be eliminated in both acidic and neutral conditions, which is no longer limited by the volatile physiological environment. Therefore, Au@Cu2O can simulate superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and glutathione peroxidase (GPx) to form a complete antioxidant system. The deigned nanoenzyme is explored in the real sample world such as A549 cells and zebrafish. This work provides theoretical and practical strategies for the construction of a complete antioxidant enzyme system.

Catalase and interleukin-6 serum elevation in a prediction of treatment-resistance in male schizophrenia patients.

BACKGROUND: Oxidative stress (OS) and neuroinflammatory pathways play an important role in the pathophysiology of schizophrenia. The present study investigated the relationship between OS, inflammatory cytokines, and clinical features in male patients with treatment-resistant schizophrenia (TRS). METHOD: We measured plasma OS parameters, including manganese-superoxide dismutase (Mn-SOD), copper/zinc-containing SOD (CuZn-SOD), total-SOD (T-SOD), malondialdehyde (MDA), catalase (CAT), and glutathione peroxidase (GSH-Px); and serum inflammatory cytokines, including interleukin (IL)- 1α, IL-6, tumor necrosis factor-alpha (TNF-α), and interferon (IFN)-γ, from 80 male patients with chronic schizophrenia (31 had TRS and 49 had chronic stable schizophrenia (CSS)), and 42 healthy controls. The severity of psychotic symptoms was evaluated using the Positive and Negative Syndrome Scale (PANSS). RESULTS: Compared with healthy controls, plasma Mn-SOD, CuZn-SOD, T-SOD, GSH-Px, and MDA levels were significantly lower, while CAT and serum IL-6 levels were higher in both TRS and CSS male patients (all P < 0.05). Significant differences in the activities of CAT (F = 6.068, P = 0.016) and IL-6 levels (F = 6.876, P = 0.011) were observed between TRS and CSS male patients after analysis of covariance. Moreover, a significant positive correlation was found between IL-6 levels and PANSS general psychopathology subscores (r = 0.485, P = 0.006) and between CAT activity and PANSS total scores (r = 0.409, P = 0.022) in TRS male patients. CAT and IL-6 levels were predictors for TRS. Additionally, in chronic schizophrenia patients, a significant positive correlation was observed between IL-6 and GSH-Px (r = 0.292, P = 0.012), and the interaction effect of IL-6 and GSH-Px was positively associated with PANSS general psychopathology scores (r = 0.287, P = 0.014). CONCLUSION: This preliminary study indicated that variations in OS and inflammatory cytokines may be involved in psychopathology for patients with chronic schizophrenia, especially in male patients with TRS.

Purification and biochemical characterization of catalase that confers protection against hydrogen peroxide induced by stressful desert environment: the Camelus Dromedarius kidney catalase.

Camel is continually exposed to stressful desert environment that enhances generation of reactive oxygen species, including hydrogen peroxide (H2O2). Catalase plays an important role in detoxification of H2O2. A highly active catalase from camel kidney was purified to homogeneity, with a specific activity of 1,774,392 U/mg protein, using ion exchange and metal chelate affinity chromatography. The molecular weight of the enzyme was 268 kDa consisting of four identical subunits of 63 kDa. The enzyme showed higher optimum temperature (45 °C) and higher activation energy (4.37 kJ mol-1). The thermodynamic parameters, ΔH, ΔG and ΔS, were determined. The effect of various metal ions and chemicals on enzyme activity was investigated. Km, Vmax, kcat and kcat/Km values for H2O2 were found to be 46 mM, 10,715,045 U/mg, 48,265,968 s-1 and 2,966,562 s-1 mM-1, respectively. Camel kidney catalase displayed higher affinity efficiency for H2O2 and can protect reduced glutathione (GSH) from oxidation by H2O2. Sodium azide was found to be a noncompetitive inhibitor of enzyme with Ki and IC50 of 17.88 µM and 20.94 µM, respectively. Camel catalase showed unique biochemical properties. Interestingly, camel catalase can protect molecules (GSH) and organ functions (kidney) from the toxic effects of H2O2 induced by stressful desert environment.

Edge-Site Engineering of Defective Fe-N4 Nanozymes with Boosted Catalase-Like Performance for Retinal Vasculopathies.

Extensive efforts are devoted to refining metal sites for optimizing the catalytic performance of single-atom nanozymes (SANzymes), while the contribution of the defect environment of neighboring metal sites lacks attention. Herein, an iron-based SANzyme (Fe-SANzyme) is rationally designed by edge-site engineering, which intensively exposes edge-hosted defective Fe-N4 atomic sites anchored in hierarchical mesoporous structures. The Fe-SANzyme exhibits excellent catalase-like activity capable of efficiently catalyzing the decomposition of H2 O2 into O2 and H2 O, with a catalytic kinetic KM value superior to that of natural catalase and reported nanozymes. The mechanistic studies depict that the defects introduce notable charge transfer from the Fe atom to the carbon matrix, making the central Fe more activated to strengthen the interaction with H2 O2 and weaken the OO bond. By performing catalase-like catalysis, the Fe-SANzyme significantly scavenges reactive oxygen species (ROS) and alleviates oxidative stress, thus eliminating the pathological angiogenesis in animal models of retinal vasculopathies without affecting the repair of normal vessels. This work provides a new way to refine SANzymes by engineering the defect environment and geometric structure around metal sites, and demonstrates the potential therapeutic effects of the nanozyme on retinal vasculopathies.

Elucidation on inhibition and binding mechanism of bovine liver catalase by nifedipine: multispectroscopic analysis and computer simulation methods.

Nifedipine (NDP), a dihydropyridine calcium antagonist, is widely used for the treatment of hypertension and angina pectoris. Catalase is a key antioxidant enzyme that is closely relevant to the level of reactive oxygen specie in vivo. Here, the research explored the effects of NDP on the conformation and catalytic function of bovine liver catalase (BLC) through enzymatic reaction kinetic techniques, multispectroscopic analysis, and computer simulation methods. Kinetic studies clarified that the NDP reduced the activity of BLC using a noncompetitive inhibition mechanism. Based on trial data, a static quenching mechanism functioned in quenching the intrinsic fluorescence of BLC. The binding constant value was (4.486 ± 0.008) × 104 M-1 (298 K) and BLC had one binding site for NDP. Tyr was prone to be exposed more to a hydrophilic environment in wake of a shift in fluorescence value. The binding reaction of BLC to NDP caused a conformational change in BLC, which in turn led to increase in the α-helix content and a decline in the ß-sheet content. Furthermore, several amino acids residues interacted with NDP by means of van der Waals forces, whereas Gln397, Asn368, Gln371, Asn384, and Pro377 formed several hydrogen bonds with NDP.

Tuning the enzyme-like activities of cerium oxide nanoparticles using a triethyl phosphite ligand.

Cerium oxide nanoparticles (CeNPs) exhibit excellent in vitro and in vivo antioxidant properties, determined by the redox switching of surface cerium ions between their two oxidation states (Ce3+ and Ce4+). It is known that ligands such as triethyl phosphite (TEP) can tune the redox behavior of CeNPs and change their biological enzyme-mimetic activities; however, the corresponding mechanism for such a behavior is completely unknown. Herein, we have studied the effect of TEP in promoting the SOD-enzyme-like activity in CeNPs with high and low Ce3+/Ce4+ ratio, which were synthesized by wet chemical and thermal hydrolysis methods, respectively, and incubated with varying concentrations of TEP. X-ray diffraction, UV-visible, photoluminescence, X-ray photoelectron spectroscopy, and Raman spectroscopy combined with DFT calculations were used to investigate the interaction of TEP on the surface of CeNPs. We observed a clear correlation between TEP concentration and the formation of surface oxygen vacancies. XPS analysis confirmed the increase in Ce3+ concentration after interaction with TEP. Moreover, we show that TEP's influence depends on the surface Ce3+/Ce4+ ratio. The superoxide dismutase-, catalase-, and oxidase-like activities of CeNPs with high Ce3+/Ce4+ ratio are not affected by TEP interaction, whereas catalase- and oxidase-like activities of CeNPs with low Ce3+/Ce4+ ratio decrease and the SOD-like activity is found to increase upon incubation with different concentrations of TEP. We also demonstrate that TEP interaction does not affect the regeneration of the CeNP surface, while the DFT calculations show that TEP facilitates the formation of defects on the surface of stoichiometric cerium oxide by reducing the oxygen vacancy formation energy. CeNPs with low Ce3+/Ce4+ ratio incubated with TEP also exhibited good antibacterial activity as compared to the CeNPs or TEP alone.

Density Functional Theory Investigation of the Biocatalytic Mechanisms of pH-Driven Biomimetic Behavior in CeO2.

There is considerable interest in the pH-dependent, switchable, biocatalytic properties of cerium oxide (CeO2) nanoparticles in biomedicine, where these materials exhibit beneficial antioxidant activity against reactive oxygen species (ROS) at a basic physiological pH but cytotoxic prooxidant activity in an acidic cancer cell pH microenvironment. While the general characteristics of the role of oxygen vacancies are known, the mechanism of their action at the atomic scale under different pH conditions has yet to be elucidated. The present work applies density functional theory (DFT) calculations to interpret, at the atomic scale, the pH-induced behavior of the stable {111} surface of CeO2 containing oxygen vacancies. Analysis of the surface-adsorbed media species reveals the critical role of pH on the interaction between ROS (•O2- and H2O2) and the defective CeO2 {111} surface. Under basic conditions, the superoxide dismutase (SOD) and catalase (CAT) biomimetic reactions can be performed cyclically, scavenging and decomposing ROS to harmless products, making CeO2 an excellent antioxidant. However, under acidic conditions, the CAT biomimetic reaction is hindered owing to the limited reversibility of Ce3+ ↔ Ce4+ and formation ↔ annihilation of oxygen vacancies. A Fenton biomimetic reaction (H2O2 + Ce3+ → Ce4+ + OH- + •OH) is predicted to occur simultaneously with the SOD and CAT biomimetic reactions, resulting in the formation of hydroxyl radicals, making CeO2 a cytotoxic prooxidant.

Photosensitive Polymeric Janus Micromotor for Enzymatic Activity Protection and Enhanced Substrate Degradation.

Immobilizing enzymes into microcarriers is a strategy to improve their long-term stability and reusability, hindered by (UV) light irradiation. However, in such approaches, enzyme-substrate interaction is mediated by diffusion, often at slow kinetics. In contrast, enzyme-linked self-propelled motors can accelerate this interaction, frequently mediated by the convection mechanism. This work reports on a new photosensitive polymeric Janus micromotor (JM) for UV-light protection of enzymatic activity and efficient degradation of substrates accelerated by the JMs. The JMs were assembled with UV-photosensitive modified chitosan, co-encapsulating fluorescent-labeled proteins and enzymes as models and magnetite and platinum nanoparticles for magnetic and catalytic motion. The JMs absorbed UV light, protecting the enzymatic activity and accelerating the enzyme-substrate degradation by magnetic/catalytic motion. Immobilizing proteins in photosensitive JMs is a promising strategy to improve the enzyme's stability and hasten the kinetics of substrate degradation, thereby enhancing the enzymatic process's efficiency.

The protective effect of natural phenolic compound on the functional and structural responses of inhibited catalase by a common azo food dye.

In this research retrieval effects of natural yellow (NY) on the performance of carmoisine (CAR) inhibited bovine liver catalase (BLC) was studied using multispectral and theoretical methods. Kinetic studies showed that CAR inhibited BLC through competitive inhibition (IC50 value of 2.24 × 10-6 M) while the addition of NY recover the activity of CAR-BLC up to 82% in comparison with the control enzyme. Circular dichroism data revealed that NY can repair the structural changes of BLC, affected by CAR. Furthermore, an equilibrium dialysis study indicated that NY could reduce the stability of the CAR-catalase complex. The surface plasmon resonance (SPR) data analysis indicated a high affinity of NY to BLC compared to CAR and the binding of NY led to a decrease in the affinity of the enzyme to the inhibitor. On the other hand, fluorescence and molecular docking studies showed that the quenching mechanism of BLC by CAR occurs through a static quenching process, and van der Waals forces and hydrogen bonding play a crucial role in the binding of CAR to BLC. MLSD data demonstrated that NY could increase the binding energy of CAR-BLC complex from -7.72 kJ mol-1 to -5.9 kJ mol-1, leading to complex instability and catalase activity salvage.

GSNOR regulates ganoderic acid content in Ganoderma lucidum under heat stress through S-nitrosylation of catalase.

As a master regulator of the balance between NO signaling and protein S-nitrosylation, S-nitrosoglutathione (GSNO) reductase (GSNOR) is involved in various developmental processes and stress responses. However, the proteins and specific sites that can be S-nitrosylated, especially in microorganisms, and the physiological functions of S-nitrosylated proteins remain unclear. Herein, we show that the ganoderic acid (GA) content in GSNOR-silenced (GSNORi) strains is significantly lower (by 25%) than in wild type (WT) under heat stress (HS). Additionally, silencing GSNOR results in an 80% increase in catalase (CAT) activity, which consequently decreases GA accumulation via inhibition of ROS signaling. The mechanism of GSNOR-mediated control of CAT activity may be via protein S-nitrosylation. In support of this possibility, we show that CAT is S-nitrosylated (as shown via recombinant protein in vitro and via GSNORi strains in vivo). Additionally, Cys (cysteine) 401, Cys642 and Cys653 in CAT are S-nitrosylation sites (assayed via mass spectrometry analysis), and Cys401 may play a pivotal role in CAT activity. These findings indicate a mechanism by which GSNOR responds to stress and regulates secondary metabolite content through protein S-nitrosylation. Our results also define a new S-nitrosylation site and the function of an S-nitrosylated protein regulated by GSNOR in microorganisms.

Structural analyses and classification of novel isoniazid resistance coupled mutational landscapes in Mycobacterium tuberculosis: a combined molecular docking and MD simulation study.

Drug resistance in Mycobacterium tuberculosis has become a major challenge to the current regime of treatment as well as to the containment of the disease globally. The molecular and genetic studies identified frequently occurring point mutations in the virulent protein such as KatG of M. tuberculosis resulted in the development of isoniazid tolerance in the pathogen. This study aims to analyze the structural basis of the disease mutations available in the literature as well as to predict novel alteration in the KatG which may cause similar deleterious effects. Around 15 experimentally derived mutations were included in this study and pathogenic mutational landscapes containing 60 site-specific alterations were predicted using the available in silico techniques. The effects of these mutations on the stability of the protein were studied and an exhaustive docking study was conducted for each classified perturbations, which identify the highest changes in the binding energies in p.Meth255Ile among experimental and p.Ala222Arg in computationally predicted mutations. Furthermore, the structural effects on these substitutions were analyzed using the principles of molecular dynamic simulations each for a 100 ns time scale, which validated the interaction studies. The outcome of this study may enable the identification of the novel drug resistance-associated point mutations which were not previously reported and may contribute significantly in a variety of experimental studies as well as facilitate the process of drug design and discovery.Communicated by Ramaswamy H. Sarma.

Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation.

Bimetallic active sites in enzymes catalyze small-molecule conversions that are among the top 10 challenges in chemistry. As different metal cofactors are typically incorporated in varying protein scaffolds, it is demanding to disentangle the individual contributions of the metal and the protein matrix to the activity. Here, we compared the structure, properties, and hydrogen peroxide reactivity of four homobimetallic cofactors (Mn(II)2, Fe(II)2, Co(II)2, Ni(II)2) that were reconstituted into a four-helix bundle protein. Reconstituted proteins were studied in solution and in crystals. All metals bind with high affinity and yield similar cofactor structures. Cofactor variants react with H2O2 but differ in their turnover rates, accumulated oxidation states, and trapped peroxide-bound intermediates. Varying the metal composition thus creates opportunities to tune the reactivity of the bimetallic cofactor and to study and functionalize reactive species.

Protein-Ligand Dissociation Rate Constant from All-Atom Simulation.

Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom molecular dynamics (MD) simulations. Random acceleration MD (τ-RAMD) was used, in which a random artificial force applied to the ligand facilitates its dissociation. We have suggested a novel approach to extrapolate such obtained dissociation times to the zero-force limit assuming never before attempted universal exponential dependence of the bond strength on the applied force, allowing direct comparison with experimentally measured values. We have found that our calculated dissociation time was equal to 36.1 s with statistically significant values distributed in the interval of 0.2-72.0 s, which quantitatively matches the experimental value of 50 ± 8 s despite the extrapolation over 9 orders of magnitude in time.